* Just the protein refs:
*/
found = DBRefUtils.selectDbRefs(false, refs);
- assertEquals(5, found.length);
+ assertEquals(4, found.length);
assertSame(ref1, found[0]);
assertSame(ref2, found[1]);
- assertSame(ref3, found[2]);
- assertSame(ref4, found[3]);
- assertSame(ref9, found[4]);
+ assertSame(ref4, found[2]);
+ assertSame(ref9, found[3]);
}
/**
seq.addDBRef(new DBRefEntry("ENSEMBLGENOMES", "0", "E2350"));
sources = new CrossRef(new SequenceI[] { seq }, al)
.findXrefSourcesForSequences(false);
- assertEquals(4, sources.size());
- assertEquals("[EMBL, EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
+ // method is patched to remove EMBL from the sources to match
+ assertEquals(3, sources.size());
+ assertEquals("[EMBLCDS, GENEDB, ENSEMBL]", sources.toString());
/*
* add a sequence to the alignment which has a dbref to UNIPROT|A1234
al.addSequence(seq2);
sources = new CrossRef(new SequenceI[] { seq, seq2 }, al)
.findXrefSourcesForSequences(false);
- assertEquals(3, sources.size());
- assertEquals("[EMBLCDS, EMBL, GENEDB]", sources.toString());
+ // method removed EMBL from sources to match
+ assertEquals(2, sources.size());
+ assertEquals("[EMBLCDS, GENEDB]", sources.toString());
}
/**
*/
SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
Mapping map = new Mapping(new Sequence("pep2", "MLAVSRG"), new MapList(
- new int[] { 1, 21 }, new int[] {
- 1, 7 }, 3, 1));
+ new int[] { 1, 21 }, new int[] { 1, 7 }, 3, 1));
DBRefEntry dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2", map);
dna1.addDBRef(dbref);
dna1.addDBRef(new DBRefEntry("EMBL", "0", "AF039662"));
dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
found = testee.searchDataset(!dna1.isProtein(), dna1, dbref, result,
acf, false); // search dataset with a protein xref from a dna
- // sequence to locate the protein product
+ // sequence to locate the protein product
assertTrue(found);
assertEquals(1, result.size());
assertSame(pep1, result.get(0));
dbref = new DBRefEntry("UNIPROT", "0", "Q9ZTS2");
found = testee.searchDataset(!pep1.isProtein(), pep1, dbref, result,
acf, false); // search dataset with a protein's direct dbref to
- // locate dna sequences with matching xref
+ // locate dna sequences with matching xref
assertTrue(found);
assertEquals(1, result.size());
assertSame(dna1, result.get(0));
public void testFindXrefSequences_withFetch()
{
SequenceI dna1 = new Sequence("AF039662", "GGGGCAGCACAAGAAC");
- dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
- dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P30419"));
- dna1.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "Q9ZTS2"));
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P30419"));
+ dna1.addDBRef(new DBRefEntry("UNIPROT", "ENA:0", "P00314"));
final SequenceI pep1 = new Sequence("Q9ZTS2", "MYQLIRSSW");
+ pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "Q9ZTS2"));
+
final SequenceI pep2 = new Sequence("P00314", "MRKLLAASG");
+ pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "P00314"));
/*
* argument false suppresses adding DAS sources
* 'spliced transcript' with CDS ranges
*/
SequenceI braf002 = new Sequence("ENST00000497784", "gCAGGCtaTCTGTTCaa");
- braf002.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3"));
+ braf002.addDBRef(new DBRefEntry("UNIPROT", "ENSEMBL|0", "H7C5K3"));
braf002.addSequenceFeature(new SequenceFeature("CDS", "", 2, 6, 0f,
null));
braf002.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, 0f,
* which happens to be true for Uniprot,PDB,EMBL but not Pfam,Rfam,Ensembl
*/
final SequenceI pep1 = new Sequence("UNIPROT|P15056", "MAAL");
+ pep1.addDBRef(new DBRefEntry("UNIPROT", "0", "P15056"));
final SequenceI pep2 = new Sequence("UNIPROT|H7C5K3", "QALF");
-
+ pep2.addDBRef(new DBRefEntry("UNIPROT", "0", "H7C5K3"));
/*
* argument false suppresses adding DAS sources
* todo: define an interface type SequenceFetcherI and mock that
*/
final SequenceI x07547 = new Sequence("EMBL|X07547", "cccAAACCCTTTGGG");
DBRefEntry dbref7 = new DBRefEntry("UNIPROT", "0", "P0CE20");
- dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE19", "KPFG"),
+ dbref7.setMap(new Mapping(new Sequence("UNIPROT|P0CE20", "PFGK"),
new MapList(map2)));
x07547.addDBRef(dbref7);
DBRefEntry dbref8 = new DBRefEntry("UNIPROT", "0", "B0BCM4");